If the point of the story is to show the evils of racism, this trope can lead to a Broken Aesop if there are in fact good in-universe reasons to discriminate against a certain type of creature (say, because they need to drink human blood in order to survive, or they genuinely don't have free will or a sense of ethics like humans do).

Also note that Tropes Are Not Bad: most people wouldn't believe in a world where elves, dwarves, aliens, etc got along with perfect harmony, because their own experiences of different groups' interactions don't bear that out. Its called Fantastic Racism for a reason.

If the racism appears to be spilling into something a little less fantastic and into something more real, it's Values Dissonance.